Most riders would be faster around a tight track with the R6 as opposed to an 03 or earlier R1. An expert rider might have been better on the R1. However, the same is true of the suzuki 750 versus the 1000. At the annual masterbike contest, the times for the two suzukis were very close to each other.
With the new R1, the difference between the R6 and R1 will probably be much smaller than in the past. But, still, it is easier to get into trouble with the R1 - so expert riders will probably be faster on the R1, the rest of us on the R6.
The R1 is the better bike! Just need practice to be able to master it.